Optimizing the codon usage of synthetic gene with QPSO algorithm

DOI10.1016/J.JTBI.2008.05.010MaRDI QIDQ1797413zbMATH OpenOpenAlexWikidataFDO

Authors Yanyan Li

Publication date 22 October 2018

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.jtbi.2008.05.010

zbMATH Keywords

codon usagequantum-behaved particle swarm optimizationsynonymous codonsynthetic gene

Mathematics Subject Classification ID

Quantum algorithms and complexity in the theory of computing (68Q12) Applications of mathematical programming (90C90) Biochemistry, molecular biology (92C40)

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Cites work

• Genetic code from tRNA point of view
• scientific article; zbMATH DE number 960162 (Why is no real title available?)
• Minimization by Random Search Techniques
• Optimality of codon usage in \textit{Escherichia coli} due to load minimization

Cited in

(10)

• A novel multiobjective quantum-behaved particle swarm optimization based on the ring model
• Efficient codon optimization with motif engineering
• Codon optimization by 0-1 linear programming
• A theoretical analysis of codon adaptation index of the \textit{Boophilus microplus bm86} gene directed to the optimization of a DNA vaccine
• Quantum-behaved particle swarm optimization for parameter optimization of support vector machine
• Chaotic quantum behaved particle swarm optimization algorithm for solving nonlinear system of equations
• COStar: A D-star Lite-based dynamic search algorithm for codon optimization
• Efficient Codon Optimization with Motif Engineering
• Multiple sequence alignment using the hidden Markov model trained by an improved quantum-behaved particle swarm optimization
• Operon structure optimization by random self-assembly

Describes a project that uses

Uses Software

• OPTIMIZER
• PISCES
• JCat
• GeMS
• Synthetic Gene Designer
• Gene Designer

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